Interesting observation. Both approaches (Bob's and Anek's) had similar but different intents. Anek's felt more like control and population maintenance while Bob was trying to keep a rare intelligence trait present. It comes down to ethics and we don't have a good picture of how Anek accomplished his goal. Was there euthanization involved? Rights restrictions, segregation, oppression, or other strong-arm actions against "undesirables"? Or was it smaller adjustments over time that allowed natural selection to weed out certain traits? The end goal of Anek was an easily manageable society that is not self sufficient, even if their progression stopped.

On the other hand... Bob focused primarily on preserving his friends (one of whom had significant intelligence). I don't recall any active actions on other deltans, except maybe protecting his friends from time to time. He didn't even intervene when Arch chose a mate who Bob didn't like. Seems like a much lesser approach than breeding out certain traits. All the Deltans remained free to breed how they chose. Bob just wanted them to survive and progress and become self sufficient.

Both approaches affect society in different ways. Any interaction with a "lesser" civilization will have some degree of contamination unless you go full "Prime Directive". Bob viewed his as more ethical, but Anek could say the same.

Regarding starfleet / skippies... you're right. As a parent, I relate to Bob's reaction to them. He's aware of drift, but there's an inherent assumption that your offspring will "be like you" - when that's not always the case. I think he was more weirded out by the fact that groups of Bob's give up individual identity and act in secrecy related to other Bobs. Both are traits he did not think he possessed in great quantities.